In a conference call with analysts in August 2005, Byrne said that "there's been a plan since we were in our teens to destroy our stock, drive it down to $6--$10 ... and even a plan for how the company would then get whacked up." He said that the conspirators were part of a "Miscreants Ball," headed by a "Sith Lord," who he refused to identify but said "he's one of the master criminals from the 1980s." Byrne said the conspiracy included hedge funds, journalists, investigators, trial lawyers, the SEC, and Eliot Spitzer. Fortune writer Bethany McLean said that Byrne had become a "hero to those who believe that short-sellers are the operators of Wall Street's ultimate black box, predators who destroy companies through innuendo, bullying, political connections--and sometimes through an illegal practice known as 'naked shorting.'" Byrne financed and largely wrote a full-page advertisement in the Washington Post which said "Naked short-selling ... is literally stealing money from the widows, retirees, and other small investors." In a letter to the Wall Street Journal in April 2006, Byrne contended that "blackguards have practiced 'failure to deliver'" of securities, were "destroying businesses and (probably) destabilizing our capital markets." Since 2005, Overstock has filed two lawsuits relating to the matters under Byrne's direction.

In the first lawsuit, filed 2005, Overstock.com filed suit against hedge fund Rocker Partners and the equities research firm, Gradient Analytics (formerly Camelback Research Alliance), saying they illegally colluded in short-selling the company while paying for negative reports to drive down share prices. The defendant (i.e. Gradient Analytics et al.) moved to have the case dismissed, however the California court ruled in August 2006 that the suit should be allowed to proceed. Gradient filed a counter-complaint against Byrne for libel. A portion of this suit was settled out of court on October 13, 2008, when Overstock.com and Gradient dropped the claims against each other after Gradient retracted allegations that Overstock's reporting methods did not comply with rules established by the FASB, stated they believed Overstock.com complied with GAAP standards, and that three directors were independent, and apologized. In December 2009, the suit against Rocker, whose name had since been changed to Copper River Partners, was settled by Copper River paying $5 million, payment of which Byrne stated he received on December 9, 2009.

Overstock.com filed a second lawsuit in 2007 against a number of large investment banks relating directly to alleged illegal naked short selling. Both cases remain in litigation.

Byrne's campaign against naked short selling and others who he feels have targeted him and his company has attracted controversy. In her article on Byrne's 2005 conference call, Bethany McLean said "From a distance he seems like a bully, accusing people who depend on their reputations of corruption. The time is rapidly approaching when he will have to deliver--both the numbers to prove that the business can make money and the facts to prove that the Sith Lord exists." In a column in the New York Times in February 2006, journalist Joseph Nocera described Byrne's actions as a "campaign of menace" and as an attempt to silence Overstock.com's critics. MarketWatch's Herb Greenberg has called Byrne the runner-up for Worst CEO of the Year two years running. One of Byrne's claims, that naked shorting can cause heavy dilution of a company's stock by creating sales untied to any specific shares, has been criticized by Wall Street Journal columnist Holman W. Jenkins. Byrne has cited Overstock.com as an example of a company whose shares have been more than 100% sold short in one quarter, but Jenkins suggests that this merely reflects Overstock.com's heavy trading volume and relatively small public float. Jenkins further argues that brokers are inherently cautious in using the practice, due to the high risk of trading shares that are not guaranteed to be available. Byrne has denied that his campaign is primarily about Overstock.com. However, Byrne has also received favorable coverage, and was featured in a Bloomberg Television show on Naked Short Selling, "Phantom Shares", in March 2007.

In March 2006, John (Jack) Byrne, chairman of Overstock.com and father of Patrick Byrne, said that he was thinking of stepping down in disagreement over the campaign against naked shorting. In April 2006, John Byrne stepped down to become vice-chairman, and in July of that year he resigned from Overstock's board of directors. In August 2008, Jack Byrne said that after "much initial skepticism" he believed his son was "right all along" about the battle and lawsuits with short-sellers and analysts.

Byrne was instrumental in Utah's passage of a law aimed at curbing naked short selling. The legislation was repealed in February 2007, after state representatives were advised that it probably would not withstand judicial scrutiny due to federal preemption. Byrne criticized the repeal, but Senate Majority Leader Curtis Bramble said that legal advisers believed that the state would lose any litigation over the law.

A Securities and Exchange Commission investigation of Gradient was initiated but then dropped in February 2007. In July 2007, two American Stock Exchange options market makers were fined and suspended for using Regulation SHO exemptions to "impermissibly engage in naked short selling" in trades involving options and stocks for their own account. Overstock shares were believed to be among the stocks traded. The market makers settled without admitting or denying the allegations. None of the defendants sued by Overstock were named in the decision, but the Dow Jones News Service said that the decision was likely to be used by Byrne in pursuing his case.

After the crisis in the North American markets in 2008, Byrne received positive press. A Salt Lake Tribune article reported that "These days, when people talk of Byrne, the word 'vindication' comes up a lot."